Variance-reduced random batch Langevin dynamics.

The random batch method is advantageous in accelerating force calculations in particle simulations, but it poses a challenge of removing the artificial heating effect in application to the Langevin dynamics. We develop an approach to solve this issue by estimating the force variance, resulting in a variance-reduced random batch Langevin dynamics. Theoretical analysis shows the high-order local truncation error of the time step in the numerical discretization scheme, consistent with the fluctuation-dissipation theorem.

Energy stable scheme for random batch molecular dynamics.

The computational bottleneck of molecular dynamics is pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but the stochastic nature of this algorithm leads to unphysical self-heating effect during the simulation. We propose an energy stable scheme (ESS) for particle systems by employing a Berendsen-type energy bath.

A Screening Condition Imposed Stochastic Approximation for Long-Range Electrostatic Correlations.

The recent random batch Ewald algorithm, originating from a stochastic approximation, performs 1 order of magnitude faster than the mainstream algorithms such as the particle-particle particle-mesh method for handling of long-range electrostatics in large-scale simulations. However, this algorithm fails to fully capture the long-range electrostatic correlations. Here, we demonstrate that, when incorporating a known screening condition in the stochastic approximation, the algorithm could be simply amended without the loss of any efficiency.

Dual-Mode Biosensor for Simultaneous and Rapid Detection of Live and Whole Based on Bioluminescence and Fluorescence Detection.

Both live and dead (S.T) are harmful to human health, but there are differences in pathological mechanism, dosage, and security. It is crucial to develop a rapid and simultaneous assay to distinguish and quantify live and dead S.

A microfluidic chip-based multivalent DNA walker amplification biosensor for the simultaneous detection of multiple food-borne pathogens.

The rapid, simultaneous, sensitive detection of the targets has important application prospects for disease diagnosis and biomedical studies. However, in practical applications, the content of the targets is usually very low, and signal amplification strategies are often needed to improve the detection sensitivity. DNAzyme-driven DNA walkers are an excellent signal amplification strategy due to their outstanding specificity and sensitivity.

A random batch Ewald method for charged particles in the isothermal-isobaric ensemble.

We develop an accurate, highly efficient, and scalable random batch Ewald (RBE) method to conduct molecular dynamics simulations in the isothermal-isobaric ensemble (the NPT ensemble) for charged particles in a periodic box. After discretizing the Langevin equations of motion derived using suitable Lagrangians, the RBE method builds the mini-batch strategy into the Fourier space in the Ewald summation for the pressure and forces such that the computational cost is reduced to O(N) per time step. We implement the method in the Large-scale Atomic/Molecular Massively Parallel Simulator package and report accurate simulation results for both dynamical quantities and statistics for equilibrium for typical systems including all-atom bulk water and a semi-isotropic membrane system.

Silencing of Circ_0135889 Restrains Proliferation and Tumorigenicity of Human Neuroblastoma Cells.

Introduction: Neuroblastoma (NB) is the most common extracranial solid tumor in infants and young children. Circular ribonucleic acid (RNA) hsa_circ_0135889 (circ_0135889; hsa_circ argonaute 2 _001) is highly expressed in multiple cancer tissues, including NB. However, its role in tumor progression of NB was unclear.

Improved Random Batch Ewald Method in Molecular Dynamics Simulations.

The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano/microscale. The method shows great potential to solve the computational bottleneck of long-range interactions, motivating a necessity to accelerate short-range components of the nonbonded interactions for a further speedup of MD simulations. In this work, we present an improved RBE method for the nonbonding interactions by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard-Jones potential.

Superscalability of the random batch Ewald method.

Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular dynamics simulations, which are major tools for problems at the nano-/micro-scale. Various algorithms are developed to calculate the pairwise Coulomb interactions to a linear scale, but poor scalability limits the size of simulated systems.

Rapid and sensitive detection of Staphylococcus aureus by using a long-period fiber grating immunosensor coated with egg yolk antibody.

The rapid and reliable detection of bacteria plays an important role in clinical and veterinary practice. A stable, label free, compact, and sensitive long-period fiber grating (LPFG) sensor based on egg yolk antibody (IgY) was proposed for the detection of Staphylococcus aureus (S. aureus).

Ion transport in electrolytes of dielectric nanodevices.

Ion transport in electrolytes with nanoscale confinements is of great importance in many fields such as nanofluidics and electrochemical energy devices. The mobility and conductance for ions are often described by the classical Debye-Hückel-Onsager (DHO) theory but this theory fails for ions near dielectric interfaces. We propose a generalized DHO theory by using the Wentzel-Kramers-Brillouin techniques for the solution of the Onsager-Fuoss equation with variable coefficients.

The Theoretical Model, Method, and Applications of Scattering Photon Burst Counting Based on an Objective Scanning Technique.

Scattering photon burst counting (SPBC) is a single-particle detection method, which is based on measuring scattering photon bursting of single nanoparticles through a detection volume of <1 fL. Although SPBC has been used for bioassays and analysis of nanoparticles, it is necessary to establish its theoretical model and develop a new detection mode in order to further enhance its sensitivity and enlarge its application fields. In this paper, we proposed a theoretical model for the confocal SPBC method and developed a novel SPBC detection mode using the fast objective scanning technique.

Random-batch list algorithm for short-range molecular dynamics simulations.

We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a full Verlet list, which introduces two-level neighbor lists for each particle such that the neighboring particles are located in core and shell regions, respectively. Direct interactions are performed in the core region.

Harmonic surface mapping algorithm for molecular dynamics simulations of particle systems with planar dielectric interfaces.

We have developed an accurate and efficient method for molecular dynamics simulations of charged particles confined by planar dielectric interfaces. The algorithm combines the image-charge method for near field with the harmonic surface mapping, which converts the contribution of infinite far-field charges into a finite number of charges on an auxiliary spherical surface. We approximate the electrostatic potential of far-field charges via spherical harmonic expansion and determine the coefficients by fitting the Dirichlet-to-Neumann boundary condition, which only requires the potential within the simulation cell.

Effects of Kinetic Dielectric Decrement on Ion Diffusion and Capacitance in Electrochemical Systems.

Diffusion of ionic components in electrolytes not only eliminates the gradients of ionic concentrations but also alters the local dielectric environment, and the coupling effect between kinetic dielectric decrement and ionic concentration gradient on the diffusion dynamics is not well understood. Herein, taking the charging process in electrical double layer systems as a case study, we conduct a multiscale investigation of ion diffusions in aqueous electrolytes by combining the dynamic density functional theory and an ion-concentration-dependent dielectric constant model. By properly considering the time evolutions of local dielectric constant coupled with ion density, we report an interesting phenomenon on the suppression of surface charge density that is not captured by conventional models.

Effect of high hydrostatic pressure on aroma components, amino acids, and fatty acids of Hami melon ( L. var. reticulatus naud.) juice.

The changes and relationships between the volatile compounds and fatty acids, and between volatile compounds and free amino acids were analyzed after they were handled by 400 and 500 MPa (45°C/10 min) high hydrostatic pressure (HHP). The volatile components of 31, 30, and 32 were detected in the untreated, 400, and 500 MPa samples, respectively. Unlike the ketones and acids, the three contents, including ester (59.

Efficient dynamic simulations of charged dielectric colloids through a novel hybrid method.

Modern particle-based simulations increasingly incorporate polarization charges arising from spatially nonuniform permittivity. For complex dielectric geometries, calculation of these induced many-body effects typically requires numerical solvers based upon boundary-element methods, which very significantly increase the required computational effort. For the special case of dielectric spheres, such as colloids or nanoparticles, we recently proposed a semianalytical spectrally accurate hybrid method that combines the method of moments, the image-charge method, and the fast multipole method.

System-integrated technology-enabled model of care to improve the health of stroke patients in rural China: protocol for SINEMA-a cluster-randomized controlled trial.

Background: Despite the significant burden of stroke in rural China, secondary prevention of stroke is suboptimal. This study aims to develop a SINEMA for the secondary prevention of stroke in rural China and to evaluate the effectiveness of the model compared with usual care.

Methods: The SINEMA model is being implemented and evaluated through a 1-year cluster-randomized controlled trial in Nanhe County, Hebei Province in China.

Harmonic surface mapping algorithm for fast electrostatic sums.

We propose a harmonic surface mapping algorithm (HSMA) for electrostatic pairwise sums of an infinite number of image charges. The images are induced by point sources within a box due to a specific boundary condition which can be non-periodic. The HSMA first introduces an auxiliary surface such that the contribution of images outside the surface can be approximated by the least-squares method using spherical harmonics as basis functions.

Accurate image-charge method by the use of the residue theorem for core-shell dielectric sphere.

An accurate image-charge method (ICM) is developed for ionic interactions outside a core-shell structured dielectric sphere. Core-shell particles have wide applications for which the theoretical investigation requires efficient methods for the Green's function used to calculate pairwise interactions of ions. The ICM is based on an inverse Mellin transform from the coefficients of spherical harmonic series of the Green's function such that the polarization charge due to dielectric boundaries is represented by a series of image point charges and an image line charge.

Ion Structure Near a Core-Shell Dielectric Nanoparticle.

A generalized image charge formulation is proposed for the Green's function of a core-shell dielectric nanoparticle for which theoretical and simulation investigations are rarely reported due to the difficulty of resolving the dielectric heterogeneity. Based on the formulation, an efficient and accurate algorithm is developed for calculating electrostatic polarization charges of mobile ions, allowing us to study related physical systems using the Monte Carlo algorithm. The computer simulations show that a fine-tuning of the shell thickness or the ion-interface correlation strength can greatly alter electric double-layer structures and capacitances, owing to the complicated interplay between dielectric boundary effects and ion-interface correlations.

Hybrid Monte Carlo and continuum modeling of electrolytes with concentration-induced dielectric variations.

The distribution of ions near a charged surface is an important quantity in many biological and material processes, and has been therefore investigated intensively. However, few theoretical and simulation approaches have included the influence of concentration-induced variations in the local dielectric permittivity of an underlying electrolyte solution. Such local variations have long been observed and known to affect the properties of ionic solution in the bulk and around the charged surface.

Self-consistent field model for strong electrostatic correlations and inhomogeneous dielectric media.

Electrostatic correlations and variable permittivity of electrolytes are essential for exploring many chemical and physical properties of interfaces in aqueous solutions. We propose a continuum electrostatic model for the treatment of these effects in the framework of the self-consistent field theory. The model incorporates a space- or field-dependent dielectric permittivity and an excluded ion-size effect for the correlation energy.

Simulation of electric double layers around charged colloids in aqueous solution of variable permittivity.

The ion distribution around charged colloids in solution has been investigated intensely during the last decade. However, few theoretical approaches have included the influence of variation in the dielectric permittivity within the system, let alone in the surrounding solvent. In this article, we introduce two relatively new methods that can solve the Poisson equation for systems with varying permittivity.